A Case for the Guardian Stones
The question came to mind when, moving through the early parts of the main quest, I came upon the Ritual Stone. I accepted it, having long agreed with this argument of the Guardian Stones being bad for you, and having an extra ability is better than none at all. Soon after, something occurred to me that made me go back to them.
Before I get into that, let me go over the reasoning behind why people consider these first stones to be inevitably bad for you. The world of Skyrim levels up as you do. That means even when you go into the final boss characters, they'd all be at level 1 if you never advance your level. I'll admit, I've noticed that things start to get really serious right around level 20. Suddenly, the whole world seems much more able to outright kill you. However, even at the base level, your skills can continue to increase. There's certainly nothing wrong with your skills being good without perks. The perks also go a long way to helping you deal with the world. As long as you focus on a particular set of skills, rather than just doing everything, you should still be able to keep up.
The key point that brought me back to these stones is that they let you increase your armor skill! Nobody seems to really think about this, since their armor rating just seems to go up naturally. The problem is that you need to actually get hit in order for your skill in armor to increase. If you ignore your armor training, you might as well not even be wearing any. It is actually ideal to get hit more at the start of the game when things are weaker, and you can stand to take more hits. Now, if I'm well rested with the appropriate Guardian Stone giving me this huge skill increase, my armor rating goes up 30% faster than normal! Suddenly, it doesn't seem like such a bad deal. Sure, the world gets stronger, but I'll be able to take those hits as easily as I ever did.
Of course, this ignores the Mage Stone, which offers no armor improvement. What it offers instead is something more subtle (which magic-users often favor, anyway). As your skill in magic goes up, the cost for your spells goes down, and I'm not even talking in regards to the perks. It's a slight decrease, but every little benefit adds up. Of course, the perks do help tremendously in this way, and this allows you to use much more effective spells. You'll always find more powerful weapons & armor just playing through the game as you level up. Spells take more effort to acquire, and even when you get them, you probably won't even be able to use them until you get the appropriate half-cost perk. Higher levels are actually really important to a wizard.